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Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science and related areas. It offers a flexible rendering framework and a powerful plugin architecture.

Features:

* Cross-Platform: Molecular builder for Windows, Linux, and Mac
* Free, Open Source: Easy to install and all source code is available (GNU GPL)
* International: Translations into Chinese, French, German, Italian, Russian, Spanish and more
* Intuitive: Built to work easily for students and advanced researchers both.
* Fast: Supports multi-threaded rendering and computation.
* Extensible: Plugin architecture for developers, including rendering, interactive tools, commands, and Python scripts
* Flexible: Features include Open Babel import of chemical files, multiple computational packages, crystals, biomolecules, etc.

It works across platforms and is used in computational chemistry, molecular modeling, bio informatics, material science and other related areas. The aim has been to make 3D molecular manipulation as easy as possible and even if your not a scientists, it's quite entertaining just creating your own different coloured structures that look good. This can be done simply by using the mouse buttons and dragging the molecules on their three axis. Probably the best aspect of this program for those with some coding knowledge is that it can be easily extended and developed via plugins. Avogadro is based on Open Babel according to the developers and in future, will also offer scripting options. The main problem you'll find is that like with many open source collaborations, it is prone to bugs and errors so it may crash at any time.